Could Syngenta's announcement that it has sequenced the rice genome have profound implications for crop biotechnology?

On January 26, agribusiness Syngenta (Basel, Switzerland), in collaboration with Myriad Genetics (Salt Lake City, UT), announced the completed sequencing of the rice genome. Syngenta does not plan to publish the data, the commercial significance of which remains unclear. Meanwhile, the public effort to sequence the rice genome, which is expected to result in publicly available data that is more accurate and complete, is being speeded up.

Myriad took eighteen months to shotgun sequence the genome of Oryza sativa japonica for Syngenta, in return for $33.5 million, plus an additional $3 million payment for completing the project six months ahead of schedule. Myriad, whose stock jumped over 20% to $80.5 the week following the news, says comparison of the sequence to six randomly chosen publicly-available bacterial artificial chromosomes (BACs) show it to be 99.5% accurate. Myriad has also aligned the sequence in a linear, unambiguous order, using BAC fingerprint data generated by the Clemson University Genome Institute (CUGI; Clemson, SC) as part of a deal funded by Novartis Agribusiness prior to its merger with Zeneca Agrochemicals to create Syngenta (Nat. Biotechnol. 18, 14, 2000). Syngenta subsidiary Torrey Mesa Research Instititute (TMRI; La Jolla, CA) analyzed this alignment, finding that the rice genome is 430 megabases long and that the 2.6 billion base pairs generated by Myriad is enough to cover it about six-fold, albeit with some gaps of 50-100 base pairs.

Researchers at TMRI have further annotated the sequence and found the twelve rice chromosomes contain 50,000 genes—something that was elucidated by “an amalgamation of [wet] data and gene predictions from [computer] programs and so forth,” according to TMRI director Steven Briggs. “We've [also] done shotgun proteomics that gives us peptides corresponding to the genes, so we've assembled a lot of computational and functional data to annotate the rice genome.”

Rice is the first commercially important crop to be sequenced, although the weed Arabidopsis thaliana was the first plant genome to be sequenced (Nat. Biotechnol. 19, 91, 2001). Mike Gale at the John Innes Institute (Colney, Norwich, UK) says that rice could be an important model because genes are very conserved between rice, maize, and wheat, and the more minor crops such as sorghum, millet, and oats. Therefore, linking quantitative traits, such as disease resistance, to genes in rice, could be translated to other crops. Syngenta says it plans to use the sequence to generate improved conventional varieties of cereal crops within five years, and biotechnologically improved crops and crop protection chemicals based on plant-specific gene targets within eight years.

However, Gale points out that “The value of the rice sequence as a model depends on how much of it is unique to rice and possibly the grasses. And that really is a big question.” But the TMRI team says it has already used in-house computer software to compare the rice genome to that of A. thaliana, and claims that 18% of A. thaliana's 25,000 genes have no apparent homology to genes in rice, and that the remaining 29,500 rice genes are unique to the grains. However, Syngenta does not plan to publish the data, the quality of which remains to be verified.

As for access to the sequence, Syngenta has said it will make its data available to commercial researchers through deals forged on a collaboration-by-collaboration basis with TMRI. Syngenta has also stated that it intends “to provide such information and technology for use in products for subsistence farmers, without royalties or fees.” According to Ronald Cantrell, director general of the International Rice Research Institute (IRRI; Los Baños, Philippines), negotiations began in early February to allow the non-profit agricultural research center royalty-free access to the data for non-commercial purposes.

Meanwhile, in response to Syngenta's news, the International Rice Genome Sequencing Project (IRGSP) has announced an acceleration of the public effort to sequence the same japonica variety of rice (Nat. Biotechnol. 17, 1057, 1999). The IRGSP is using BACs to sequence each chromosome separately—a method that is slower but considered more thorough than shotgun sequencing—and has so far published 30 megabases of sequence that is gapless, has ten times coverage, and is 99.99% accurate (http://rgp.dna.affrc.go.jp/Seqcollab.html). The goal for completing sequencing in this manner was 2004, but now the group plans to speed it up to “the shortest possible time,” although it is not clear how much additional funding will be provided by the governments of the 11 participating nations. In the meantime, the IRGSP says it will immediately publish all 99.99% accurate sequence it already has, even if it contains gaps, and reportedly plans to finish sequencing all 12 rice chromosomes to this degree by the end of 2001—a goal that will be achieved, in part, using rice genome sequence donated by Monsanto (Nat. Biotechnol. 18, 484, 2000). However, the IRGSP does not plan to buy access to Syngenta's data.